Variant report

Variant	rs1079230
Chromosome Location	chr4:54525830-54525831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1107027	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1477875	0.85[ASN][1000 genomes]
rs1477876	0.92[EUR][1000 genomes]
rs1546526	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1972815	0.89[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1996005	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2164266	0.87[ASN][1000 genomes]
rs2572283	0.92[EUR][1000 genomes]
rs2572291	0.85[ASN][1000 genomes]
rs2572299	0.85[ASN][1000 genomes]
rs2590780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2590816	0.89[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2590823	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2616386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2616410	0.81[EUR][1000 genomes]
rs2668516	0.92[EUR][1000 genomes]
rs2668521	0.85[ASN][1000 genomes]
rs2668524	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668529	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668548	0.91[EUR][1000 genomes]
rs2668549	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668557	0.87[EUR][1000 genomes]
rs2668566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7686480	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs907510	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1079230	TXNDC9	cis	parietal	SCAN
rs1079230	FIP1L1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54522200-54526000	Weak transcription	Gastric	stomach
2	chr4:54522200-54526000	Weak transcription	Right Atrium	heart
3	chr4:54524000-54526600	Enhancers	Fetal Heart	heart
4	chr4:54524200-54526200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:54524200-54526400	Enhancers	NHDF-Ad	bronchial
6	chr4:54525400-54526400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:54525400-54526400	Enhancers	Stomach Mucosa	stomach

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